Setting skip-innodb does disable the InnoDB Storage Engine, but that does not convert the tables.
You need to script the conversion of all the tables.
STEP #1
Comment out the skip-innodb
[mysqld]
#skip-innodb
STEP #2
service mysql restart
STEP #3
Execute the Following Script snf View Results
CONVERT_SCRIPT=/tmp/InnoDBConversionToMyISAM.sql
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') "
SQL="${SQL} FROM information_schema.tables "
SQL="${SQL} WHERE engine='InnoDB' AND table_schema <> 'mysql'"
mysql -uroot -p -ANe"${SQL}" > ${CONVERT_SCRIPT}
STEP #4
View the script
vi /tmp/InnoDBConversionToMyISAM.sql
or
less /tmp/InnoDBConversionToMyISAM.sql
If you like the contents, then ...
STEP #5
Login to mysql and run
mysql> source /tmp/InnoDBConversionToMyISAM.sql
STEP #6
Uncomment out the skip-innodb
[mysqld]
skip-innodb
STEP #7
service mysql restart
STEP #8
There is no STEP 8. That's it !!!
Give it a Try !!!